CC=g++
CFLAGS=-Wall -Werror -pedantic-errors -std=c++0x 
CFLAGS+=-O3
#CFLAGS+=-O0 -g

all: motif

motif: motif.cpp
	$(CC) $(CFLAGS) -lboost_chrono motif.cpp -lboost_program_options -lboost_system -lboost_timer -ggdb -o motif-finder

clean:
	rm -f *.o motif-finder

run:
	./motif-finder -I ThreeGenes.txt -L 5 -O out.txt -T 1; cat out.txt;